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26192 COVID 19 Nucleic Acid Test (NAT) PCR

COVID 19 Nucleic Acid Test (NAT) PCR
Test Code: COV19
Synonyms/Keywords

​COVID 19 PCR, SARS-CoV-2, Coronavirus

Useful For

This is a qualitative PCR test for the detection of nucleic acid in nasopharyngeal swabs from patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).  Patients may have mild to severe respiratory illness with symptoms of sore throat, cough, fever and shortness of breath and many have had complications including pneumonia. Patients may also be asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 or asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings.

Please refer to the MCHS COVID-19 Testing Algorithm for COVID-19 Testing Process details. Clinicians are encouraged to use their judgment based on evolving epidemiology and guidance from CDC in combination with the above testing algorithm.  

NOTE: Two test pathways are available for this test code based upon the clinical necessity for testing.  Refer to the MCHS COVID-19 Test Kit Selection for specimen collection guidance:

  1. RAPID – Urgent/STAT, green labeled collection kit (3 hrs) pathway
  2. ROUTINE – (Including Pre-Procedure testing scheduled to allow 48 hours prior to procedure) High through-put, purple labeled collection kit (up to 48 hrs) pathway

    All test results are reported to the Wisconsin Electronic Disease Surveillance System (WEDSS).  Confirmed and suspected COVID-19 disease is a Category 1 reportable condition in Wisconsin.
Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)

​Nasopharyngeal swab

Routine

Purple labeled

Azer Saline (PBS) Wet Swab Collection Kit provided by Marshfield Labs

UTM Universal Viral Transport-BD, M6 Viral Transport, Xpert VTM​One nasopharyngeal swab ​One nasopharyngeal swab ​One nasopharyngeal swab

​Nasopharyngeal swab

Stat

​UTM Universal Viral Transport-BD or Sigma Saline

M6 Viral Transport, Xpert VTM Copan Eswab (Liquid Amies)​One nasopharyngeal swab​One nasopharyngeal swab​One nasopharyngeal swab
Collection Processing Instructions

 Marshfield Labs Wet Swab Collection Kit- Purple Labeled, High throughput routine testing including Pre-Procedure testing scheduled to allow 48 hours prior to procedure:

Collect a nasopharyngeal specimen using the NP swab. Place swab into the Azer buffered saline transport tube and carefully break off the swab shaft against the side of the tube at the score line. Discard the top portion of the swab shaft. Securely close the snap cap of tube.

Transport specimen at 2-8°C to Marshfield Labs as soon as possible.  If specimen cannot be tested within 72 hours of collection, it should be frozen at -70°C or colder until tested.  Testing is batched throughout the day.

Alternative collection kits – Green Labeled, Respiratory Urgent or ASAP testing: 

Collect one (1) nasopharyngeal swab (sterile polyester tipped swab with flexible shaft). Place in acceptable transport media, breaking off the swab shaft at the score line. Send specimen in transport medium, and transport bio-bag. Send to lab refrigerated.

Acceptable Body Sites

  Nasopharyngeal

Acceptable Specimen Types

​Nasopharyngeal swab 

Specimen Stability Information
Specimen TypeTemperatureTime
​Nasopharyngeal swab​refrigerate​<=72 hrs
​frozen​>72 hrs
Rejection Criteria
Specimens on cotton or calcium alginate tipped swabs
​Swabs with wooden shaft
​Specimens in transport media other than those listed above
Performing Laboratory Information
Performing LocationDay(s) Test PerformedAnalytical Time​Methodology/Intrumentation
​Marshfield ​

Monday through Sunday

Urgent/STAT pathway, turn time within 3-hours of arrival in lab

 

Routine or Pre-Op testing Pathway, turn time within 72 hours of collection dependent on location/courier timing

  ​

 

Nucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin

 

Nucleic Acid Test (NAT); Transcription Mediated Amplification (TMA) / Hologic

​​​Eau Claire​​

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​​3 hrs​​Nucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
Rice Lake​

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
Park Falls

​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
Weston

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCRNucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
​Neillsville

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
​Ladysmith

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
​Minocqua

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid 

 

Test Information

Marshfield Labs COVID-19 Nucleic Acid Test assays are Emergency Use Authorization (EUA) assays performed on multiple platforms.

MCHS Laboratory Summary on SARS-COV-2 Assay Sensitivity and Specificity

The current SARS-COV-2 PCR tests used at MCHS have been authorized for use by regulatory authorities including the FDA and CDC.  These tests are highly specific (no false-positives) and are considered to be very sensitive, approaching 100%, during symptomatic disease when high titers of viral target are present, including directly before symptoms appear and following symptom resolution for several days.  Analytic sensitivity of our assays was determined to be <5 copies of viral genomic RNA per microliter of sample and the assay has been validated against a panel of specimens provided by the Wisconsin State Laboratory of Hygiene (WSLH).  Appropriate collection technique is a critical variable for best test performance. 

Assays performed at MCHS use validated gene targets and reagents, strict quality control, and qualified testing personnel.  Results generated are comparable to those produced by public health and academic laboratories nationally. Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions.  Negative results must be combined with clinical observations, patient history, and epidemiological information.

Detection of Genetic Variants of SARS-COV-2

Several variant strains of SARS-COV-2 have recently emerged. Test manufacturers, CDC and the WSLH are constantly evaluating assay ability to detect variant strains and regularly share updates with clinical laboratories nationwide. Currently, all recognized variant strains are being detected by our testing methods.  The reported test results will not, however, differentiate between the typical pandemic strain and that of a SARS-COV-2 variant strain.  Further genetic characterization by whole genome sequencing is required to identify which variant is present.

Marshfield Labs Partnership with WSLH on Surveillance for Genetic Variants of SARS-COV-2

Wisconsin Department of Public Health, WSLH and partner laboratories are conducting active surveillance for novel and variant SARS-COV-2 strains using whole genome sequencing. Marshfield Labs is supporting this surveillance effort by selecting positive specimens from geographically dispersed Wisconsin locations, hospitalized patients, vaccine break-through cases, and re-infected patients for surveillance sequencing.  Marshfield Clinic Research Institute will perform the sequencing surveillance and report their results to the Wisconsin Department of Health Services (WDHS). 

Note that sequencing results will not be reported to the Provider or the patient. Sequencing is performed strictly for public health surveillance purposes and is not meant to advise patient care.

 

Reference Range Information
Performing LocationReference Range
All Sites

​Negative

Interpretation

Positive – SARS-CoV-2 nucleic acid detected.

Negative – No SARS-CoV-2 nucleic acid detected.

Indeterminate - Result is indeterminate due to a PCR inhibitor present in the specimen. Consider repeat specimen if clinically indicated.

Inconclusive - Result of testing is inconclusive. Laboratory performed repeat testing, but failed to provide a negative or positive result that may be due to interfering substances, lack of sufficient viral target because sample is either too early in the infection process or after most of it has been cleared, collection-associated problems, or other limitations. The result cannot be called positive or negative.

Consider submitting a repeat specimen if clinically indicated. 

Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
U0002​1​Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]
​U0003​1Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) COVID-19 testing utilizing high-throughput technology
Synonyms/Keywords

​COVID 19 PCR, SARS-CoV-2, Coronavirus

Ordering Applications
Ordering ApplicationDescription
CernerCOVID 19 Nucleic Acid Test (NAT) PCR
​COMCOVID 19 Nucleic Acid Test (NAT) PCR
If the ordering application you are looking for is not listed, contact your local laboratory for assistance.
Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)

​Nasopharyngeal swab

Routine

Purple labeled

Azer Saline (PBS) Wet Swab Collection Kit provided by Marshfield Labs

UTM Universal Viral Transport-BD, M6 Viral Transport, Xpert VTM​One nasopharyngeal swab ​One nasopharyngeal swab ​One nasopharyngeal swab

​Nasopharyngeal swab

Stat

​UTM Universal Viral Transport-BD or Sigma Saline

M6 Viral Transport, Xpert VTM Copan Eswab (Liquid Amies)​One nasopharyngeal swab​One nasopharyngeal swab​One nasopharyngeal swab
Collection Processing

 Marshfield Labs Wet Swab Collection Kit- Purple Labeled, High throughput routine testing including Pre-Procedure testing scheduled to allow 48 hours prior to procedure:

Collect a nasopharyngeal specimen using the NP swab. Place swab into the Azer buffered saline transport tube and carefully break off the swab shaft against the side of the tube at the score line. Discard the top portion of the swab shaft. Securely close the snap cap of tube.

Transport specimen at 2-8°C to Marshfield Labs as soon as possible.  If specimen cannot be tested within 72 hours of collection, it should be frozen at -70°C or colder until tested.  Testing is batched throughout the day.

Alternative collection kits – Green Labeled, Respiratory Urgent or ASAP testing: 

Collect one (1) nasopharyngeal swab (sterile polyester tipped swab with flexible shaft). Place in acceptable transport media, breaking off the swab shaft at the score line. Send specimen in transport medium, and transport bio-bag. Send to lab refrigerated.

Acceptable Body Sites

  Nasopharyngeal

Acceptable Specimen Types

​Nasopharyngeal swab 

Specimen Stability Information
Specimen TypeTemperatureTime
​Nasopharyngeal swab​refrigerate​<=72 hrs
​frozen​>72 hrs
Rejection Criteria
Specimens on cotton or calcium alginate tipped swabs
​Swabs with wooden shaft
​Specimens in transport media other than those listed above
Useful For

This is a qualitative PCR test for the detection of nucleic acid in nasopharyngeal swabs from patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).  Patients may have mild to severe respiratory illness with symptoms of sore throat, cough, fever and shortness of breath and many have had complications including pneumonia. Patients may also be asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 or asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings.

Please refer to the MCHS COVID-19 Testing Algorithm for COVID-19 Testing Process details. Clinicians are encouraged to use their judgment based on evolving epidemiology and guidance from CDC in combination with the above testing algorithm.  

NOTE: Two test pathways are available for this test code based upon the clinical necessity for testing.  Refer to the MCHS COVID-19 Test Kit Selection for specimen collection guidance:

  1. RAPID – Urgent/STAT, green labeled collection kit (3 hrs) pathway
  2. ROUTINE – (Including Pre-Procedure testing scheduled to allow 48 hours prior to procedure) High through-put, purple labeled collection kit (up to 48 hrs) pathway

    All test results are reported to the Wisconsin Electronic Disease Surveillance System (WEDSS).  Confirmed and suspected COVID-19 disease is a Category 1 reportable condition in Wisconsin.
Reference Range Information
Performing LocationReference Range
All Sites

​Negative

Interpretation

Positive – SARS-CoV-2 nucleic acid detected.

Negative – No SARS-CoV-2 nucleic acid detected.

Indeterminate - Result is indeterminate due to a PCR inhibitor present in the specimen. Consider repeat specimen if clinically indicated.

Inconclusive - Result of testing is inconclusive. Laboratory performed repeat testing, but failed to provide a negative or positive result that may be due to interfering substances, lack of sufficient viral target because sample is either too early in the infection process or after most of it has been cleared, collection-associated problems, or other limitations. The result cannot be called positive or negative.

Consider submitting a repeat specimen if clinically indicated. 

For more information visit:
Performing Laboratory Information
Performing LocationDay(s) Test PerformedAnalytical Time​Methodology/Intrumentation
​Marshfield ​

Monday through Sunday

Urgent/STAT pathway, turn time within 3-hours of arrival in lab

 

Routine or Pre-Op testing Pathway, turn time within 72 hours of collection dependent on location/courier timing

  ​

 

Nucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin

 

Nucleic Acid Test (NAT); Transcription Mediated Amplification (TMA) / Hologic

​​​Eau Claire​​

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​​3 hrs​​Nucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
Rice Lake​

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
Park Falls

​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
Weston

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCRNucleic Acid Test (NAT); Real-Time RT-PCR/ DiaSorin
​Neillsville

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
​Ladysmith

​​Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid
​Minocqua

Monday through Sunday

Urgent/STAT Pathway only

Limited testing capacity.

​3 hrsNucleic Acid Test (NAT); Real-Time RT-PCR/ Cepheid 

 

For billing questions, see Contacts
Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
U0002​1​Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]
​U0003​1Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) COVID-19 testing utilizing high-throughput technology
For most current information refer to the Marshfield Laboratory online reference manual.